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- PDB-6q3w: Structure of human galactokinase 1 bound with Ethyl 1-(2-pyraziny... -

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Basic information

Entry
Database: PDB / ID: 6q3w
TitleStructure of human galactokinase 1 bound with Ethyl 1-(2-pyrazinyl)-4-piperidinecarboxylate
ComponentsGalactokinase
KeywordsTRANSFERASE / GALK1 / fragment / fragment-bound / galactokinase 1 / sugar kinase
Function / homology
Function and homology information


glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / Galactose catabolism / galactose binding / galactose metabolic process / galactose catabolic process via UDP-galactose / extracellular exosome ...glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / Galactose catabolism / galactose binding / galactose metabolic process / galactose catabolic process via UDP-galactose / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal ...Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Chem-HFK / ethyl 1-pyrazin-2-ylpiperidine-4-carboxylate / Galactokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.962 Å
AuthorsMackinnon, S.R. / Bezerra, G.A. / Zhang, M. / Foster, W. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Arrowsmith, C. / Edwards, A. / Bountra, C. ...Mackinnon, S.R. / Bezerra, G.A. / Zhang, M. / Foster, W. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Brennan, P. / Lai, K. / Yue, W.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: To Be Published
Title: Structure of human galactokinase 1 bound with Ethyl 1-(2-pyrazinyl)-4-piperidinecarboxylate
Authors: Mackinnon, S.R. / Bezerra, G.A. / Zhang, M. / Foster, W. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Brennan, P. / Lai, K. / Yue, W.W.
History
DepositionDec 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactokinase
B: Galactokinase
C: Galactokinase
D: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,11411
Polymers168,2874
Non-polymers1,8277
Water11,548641
1
A: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6023
Polymers42,0721
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6023
Polymers42,0721
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8384
Polymers42,0721
Non-polymers7663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galactokinase


Theoretical massNumber of molelcules
Total (without water)42,0721
Polymers42,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.262, 114.807, 120.818
Angle α, β, γ (deg.)90.000, 100.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Galactokinase / Galactose kinase


Mass: 42071.820 Da / Num. of mol.: 4 / Mutation: K252A, E253A, L235P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALK1, GALK / Plasmid: pNIC24-Bsa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P51570, galactokinase
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-HFK / 2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclohexane]-5-one


Mass: 350.414 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H22N4O2
#4: Chemical ChemComp-HGE / ethyl 1-pyrazin-2-ylpiperidine-4-carboxylate


Mass: 235.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of:sodium formate, ...Details: 0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of:sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate and sodium oxamate).
PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.96→82.56 Å / Num. obs: 139659 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.075 / Rrim(I) all: 0.14 / Net I/σ(I): 7.2 / Num. measured all: 472410 / Scaling rejects: 2355
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.96-2.073.41.6170129203660.4451.0181.910.999.7
6.2-82.563.30.0331486745230.9980.0220.0422.799.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WUU

1wuu


Resolution: 1.962→82.556 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.82
RfactorNum. reflection% reflection
Rfree0.2547 7029 5.04 %
Rwork0.2316 --
obs0.2328 139485 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.99 Å2 / Biso mean: 51.2843 Å2 / Biso min: 21.92 Å2
Refinement stepCycle: final / Resolution: 1.962→82.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10688 0 131 641 11460
Biso mean--50.79 50.05 -
Num. residues----1523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411029
X-RAY DIFFRACTIONf_angle_d0.91115078
X-RAY DIFFRACTIONf_chiral_restr0.0321792
X-RAY DIFFRACTIONf_plane_restr0.0041985
X-RAY DIFFRACTIONf_dihedral_angle_d13.1143814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9615-1.98380.46042350.40214467470299
1.9838-2.00710.38562210.37643684589100
2.0071-2.03160.36722590.37244124671100
2.0316-2.05730.35582500.34934361461199
2.0573-2.08440.35142740.33074381465599
2.0844-2.1130.35672210.32974375459699
2.113-2.14320.34342370.31434371460899
2.1432-2.17510.32472280.3034363459199
2.1751-2.20910.35052240.29784443466799
2.2091-2.24540.34622430.29854379462299
2.2454-2.28410.30622350.29344396463199
2.2841-2.32560.29642480.27564400464899
2.3256-2.37030.29772170.26644405462299
2.3703-2.41870.31432400.25254390463099
2.4187-2.47130.27932260.24934412463899
2.4713-2.52880.27452200.24844468468899
2.5288-2.59210.26542380.239943814619100
2.5921-2.66220.26592440.24344034647100
2.6622-2.74050.28812290.248744534682100
2.7405-2.8290.2722490.248644074656100
2.829-2.93010.28282170.238844614678100
2.9301-3.04740.28532310.23934403463499
3.0474-3.18610.25642250.230244614686100
3.1861-3.35410.25232120.2344124624100
3.3541-3.56420.2412270.22354439466699
3.5642-3.83940.22352540.20564408466299
3.8394-4.22580.21352280.19414399462798
4.2258-4.83720.19322390.17414430466999
4.8372-6.09410.21952290.20244924721100
6.0941-82.62870.19232290.19124516474599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2236-0.4980.1541.9641.84963.58260.0267-0.1938-0.4721-0.2555-0.0165-0.06230.6091-0.18280.07160.8761-0.1327-0.11160.48260.08470.4138-25.9043-26.0772-3.2942
21.59430.04540.14211.3042-0.16522.94530.074-0.1556-0.00850.10930.085-0.11920.2015-0.0748-0.08860.24340.0123-0.03110.2556-0.02580.296-24.74-12.9976-18.145
30.9818-0.16480.36430.5789-0.27813.49550.0655-0.2799-0.14940.31060.1436-0.17020.3033-0.184-0.2380.4432-0.0016-0.07350.28580.01630.3116-22.2669-14.8743-4.8345
44.0401-0.7051-0.16323.8567-0.24993.75220.0346-0.19830.26210.47090.1422-0.4959-0.4163-0.1197-0.21040.41390.0575-0.06020.3253-0.07810.324-21.2933-2.9853-2.8081
51.2171-0.34440.27771.3413-0.34523.5270.0703-0.08770.05990.12740.0757-0.06490.113-0.4529-0.12640.2487-0.0012-0.01250.2488-0.02240.2744-26.7288-9.4911-16.1121
61.23630.45-0.14412.99520.76041.7115-0.1260.17480.10860.00270.293-0.25260.13880.2473-0.10970.29810.0049-0.00390.3308-0.02520.3411-13.8974-12.3161-26.9732
71.05950.0207-0.17523.15390.32243.47920.12220.70980.3018-1.0207-0.1151-0.4813-0.57330.29810.01370.6263-0.0240.05940.53020.10980.4965-15.67523.563-41.3174
84.20870.60560.32373.60820.4492.9971-0.01890.7092-0.0911-0.24790.0796-0.15750.09620.1284-0.08040.31060.03490.02610.3937-0.04040.2538-18.962-12.8654-38.9456
91.0596-0.1326-0.04120.7104-0.03861.217-0.08850.1777-0.01920.07560.3863-0.31990.49980.3939-0.28130.420.1198-0.04020.3786-0.15390.4479-11.4439-20.5388-32.6227
100.12610.47420.45573.32311.23861.89060.16240.0646-0.3117-0.01680.1081-0.39430.97760.4982-0.1790.83770.1753-0.10430.3701-0.11330.4811-15.8611-31.6831-30.6891
113.02-1.5276-0.24771.94281.2093.4140.1225-0.5493-0.53830.10270.14550.1120.8752-0.0653-0.22750.5729-0.0437-0.11130.30180.05960.4106-23.313-24.579-17.6895
121.05040.47920.7860.23370.31580.8015-0.2864-0.29680.10370.80820.26280.375-0.6721-0.2024-0.19420.91270.33420.01420.7112-0.07220.3311-7.6964-47.3418-24.7213
131.2316-0.41170.18411.286-0.29323.5084-0.1044-0.4282-0.09360.24190.26570.2402-0.0568-0.1294-0.160.55540.16540.04720.42820.04280.3453-9.7378-57.2438-36.9231
140.9545-0.352-0.11524.0195-1.73481.694-0.1029-0.4635-0.24840.67170.36021.0906-0.2831-0.9939-0.17110.55490.20270.18270.85720.280.7791-23.9491-59.5387-28.8276
151.37010.02980.41222.5571-0.57833.4805-0.108-0.6054-0.50790.28830.35480.7366-0.2087-0.5883-0.0960.42720.12510.10890.48260.15970.4725-13.3478-61.1713-31.2236
161.4798-0.22390.05482.0068-0.3251.89050.1956-0.1891-0.4442-0.2344-0.03370.35640.236-0.025-0.10030.51750.0943-0.01960.31290.04520.4093-8.8688-64.501-43.5894
172.28810.65470.80383.08640.07812.2287-0.1687-0.34390.0317-0.23070.220.64640.0791-0.4052-0.01590.51030.0184-0.07260.39760.08980.4133-14.3724-52.8726-53.3318
181.0884-1.33150.64271.7666-0.94491.1503-0.00060.2918-0.2157-0.10850.07880.1360.60920.0092-0.09110.6368-0.0925-0.0320.4731-0.03830.3726-15.2052-64.197-70.2631
190.8190.21640.82281.13860.05022.6213-0.23290.10230.13280.02910.10030.0994-0.46180.13030.09440.57770.0774-0.00880.3208-0.00680.3174-7.0325-46.7172-54.2088
202.1094-1.19521.07711.7867-0.4972.16790.13520.1439-0.10380.1013-0.0485-0-0.09570.2064-0.08090.45180.0534-0.05820.265-0.01140.247313.6096-70.4607-29.3388
210.3868-0.53320.64241.3712-0.32012.14060.67121.0952-0.3234-0.3684-0.7317-0.0135-0.1640.90760.01240.57110.3425-0.0150.858-0.05920.433623.7821-76.0725-50.1685
221.7288-0.76270.08150.9104-0.25930.18760.87111.0791-1.479-0.6168-0.84120.5785-0.13280.2565-0.07580.84060.4619-0.32260.6113-0.46630.676613.7704-85.7876-47.9064
230.1591-0.2522-0.02351.4537-0.85390.95630.0959-1.2973-0.24-0.2227-0.11710.51320.4413-0.6617-0.18770.3343-0.17880.12161.28370.2280.400518.9768-14.4388-13.5415
240.36810.3305-0.2512.6165-0.97122.01550.3353-0.7628-0.5957-0.212-0.3325-0.0340.4923-0.736-0.0060.4416-0.1163-0.01190.90270.24640.583823.6257-17.5902-17.7924
251.85730.362-0.39651.8251.67044.0298-0.53650.38940.1503-0.24140.23740.31731.0974-0.52120.34850.6758-0.15960.03820.3935-0.04930.306313.9799-8.5987-38.9448
262.45531.4287-1.171.459-0.9622.1435-0.1079-0.13880.8175-0.10750.04160.26880.1121-0.1940.04380.2330.0195-0.050.2782-0.08520.425516.57832.4344-30.429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )A2 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 50 )A25 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 91 )A51 - 91
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 124 )A92 - 124
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 212 )A125 - 212
6X-RAY DIFFRACTION6chain 'A' and (resid 213 through 249 )A213 - 249
7X-RAY DIFFRACTION7chain 'A' and (resid 250 through 271 )A250 - 271
8X-RAY DIFFRACTION8chain 'A' and (resid 272 through 316 )A272 - 316
9X-RAY DIFFRACTION9chain 'A' and (resid 317 through 350 )A317 - 350
10X-RAY DIFFRACTION10chain 'A' and (resid 351 through 371 )A351 - 371
11X-RAY DIFFRACTION11chain 'A' and (resid 372 through 392 )A372 - 392
12X-RAY DIFFRACTION12chain 'B' and (resid 2 through 24 )B2 - 24
13X-RAY DIFFRACTION13chain 'B' and (resid 25 through 77 )B25 - 77
14X-RAY DIFFRACTION14chain 'B' and (resid 78 through 115 )B78 - 115
15X-RAY DIFFRACTION15chain 'B' and (resid 116 through 156 )B116 - 156
16X-RAY DIFFRACTION16chain 'B' and (resid 157 through 212 )B157 - 212
17X-RAY DIFFRACTION17chain 'B' and (resid 213 through 250 )B213 - 250
18X-RAY DIFFRACTION18chain 'B' and (resid 251 through 271 )B251 - 271
19X-RAY DIFFRACTION19chain 'B' and (resid 272 through 392 )B272 - 392
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 212 )C2 - 212
21X-RAY DIFFRACTION21chain 'C' and (resid 213 through 271 )C213 - 271
22X-RAY DIFFRACTION22chain 'C' and (resid 272 through 392 )C272 - 392
23X-RAY DIFFRACTION23chain 'D' and (resid 8 through 107 )D8 - 107
24X-RAY DIFFRACTION24chain 'D' and (resid 108 through 212 )D108 - 212
25X-RAY DIFFRACTION25chain 'D' and (resid 213 through 272 )D213 - 272
26X-RAY DIFFRACTION26chain 'D' and (resid 273 through 392 )D273 - 392

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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